Neo defeates Smith in such a way that Smith managed to replicate himself, which led to him being uncontrollably powerful thus the machines needed Neo’s help so they made a deal and, ultimately, peace between humans and the machines.
(long breathe)

But Neo had to make a choice at some point (during the Architect scene):

Either go to the source (destroy Zion and free 12 new humans)

Go back in the matrix and ... defeat Smith.

However, what would have happened if Neo would have chosen to go to the source? How would have the machines handled Smith in that variation?

Or, the other way around, what would have happened if Smith was really defeated and Neo went back into the Matrix to save Trinity? How else could he have saved Zion?

Lastly, assuming that these two options were available in previous matrix versions, why would the previous versions of Neo (who is known were not in love) ever choose to go back in the matrix?

All in all, was this the only matrix version in which Zion and the machines could’ve made peace?

Many good questions generate some degree of opinion based on expert experience, but answers to this question will tend to be almost entirely based on opinions, rather than facts, references, or specific expertise. If this question can be reworded to fit the rules in the help center, please edit the question.

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Too many opinion based questions in one question.
– RahulFeb 25 '18 at 12:54

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@Rahul I know the rules. Please focus on the last question. The other ones were just to build the last one
– AdelinFeb 25 '18 at 13:05

Not sure how the last one isn't opinion-based, to be honest. We only get see "this" version of the matrix in the films, so we have no canon basis to say what may or may not have happened in other versions.
– Steve-OFeb 25 '18 at 22:32

@Steve-O - It is hinted at though, for example, The Architect knew Neo's love for Trinity was greater and specific to him, programs from previous versions survive to the current version, the Ones before Neo all went to the source, Zion was restarted 5 times.
– user62053Feb 25 '18 at 22:57

1 Answer
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I don't think Neo's(Reeves) version of the Matrix was the only one where peace could be established with the humans and machines. (In this context, peace is only referring to the characters and world in the movies, it's a stretch to even say there is peace if you include the video games).

I do think the machines are prepared of a number of situations all of which will benefit them or in which they have control. Remember when Neo goes to the machine city and meets the giant machine, the machine loudly says

We don't need you! We need nothing!

The whole purpose of Neo was to give humans false hope that someone with extraordinary powers will come and save them, and to use his code to reset the matrix. For the machines, this is the ideal situation.

The Architect states

They're levels of survival the machines we are willing to accept.

In this situation it's a world without humans.

Now, other situations can have consequences the machines are prepared for but probably want to avoid, because it could severally damage the foundation of the matrix world or take up a large amount of resources that they simply don't have or can't reuse right away.

why would the previous versions of Neo (who is known were not in love)
ever chose to go back in the matrix?

As pointed out by the by the Architect, Neo's love is far more specific(Trinity) while the other Ones's wanted to save everyone. The other One's had no real reason to reject what the machines wanted them to do. Up until Neo, the other Ones's proceeded accordingly, because the Matrix is still there, and people are still searching for the One.

what would have happened if Neo would have chosen to go to the source?
How would have the machines handled Smith in that variation?

Same as always, the Matrix gets reset and admin control or total control goes back to the machines, and then they can eradicate him(much as they did at the end of Revolutions). Remember, Smith had a little more control than previous versions after he attempted to assimilate Neo, as he pointed out, a piece of code could have been imprinted, over written or copied. Given his new found powers, he probably found a way to prevent the machines from deleting him.

Because Neo didn't go to the source, the matrix couldn't be reset and Smith is now a virus.

Or, the other way around, what would have happened if Smith was really
defeated and Neo went back into the Matrix to save Trinity? How else
could he have saved Zion?

If Smith is really defeated and Neo instead went to save Trinity, I doubt the machine couldn't proceed, I believe machines had a backup plan (probably insert the code themselves or create an emergency program to do it for them), but the ideal situation is for the One to choose to save Zion and the cycle is repeated over again.